List of available software on Sockeye

Updated October 4th, 2019

AI: Artificial intelligence BIO: Bioinformatic libraries & apps CHEM: Chemistry libraries & app GEO: Geography libraries & apps IO: Input/output software 

M: MPI implementations MATH: Mathematical libraries PHYS: Physics libraries & apps T: Tools for development VIS: Visualisation software

Name

Version

Description

Software Group

AnsysEM

19.5

Ansys Electronics and Electrodynamics for research simulation. Provided for use by UBC researchers by a license through APSC. https://ansys.license.apsc.ubc.ca/

Homepage: https://www.ansys.com/products/electronics

PHYS

atlas

3.10.2

Automatically Tuned Linear Algebra Software, generic shared ATLAS is an
approach for the automatic generation and optimization of numerical
software. Currently ATLAS supplies optimized versions for the complete
set of linear algebra kernels known as the Basic Linear Algebra
Subroutines (BLAS), and a subset of the linear algebra routines in the
LAPACK library.

Homepage: http://math-atlas.sourceforge.net/

MATH

bazel

0.17.2

Bazel is Google's own build tool

Homepage: https://www.bazel.io

T

beast1

1.10.4

BEAST is a cross-platform program for Bayesian analysis of molecular
sequences using MCMC.

Homepage: http://beast.community/

BIO

beast2

2.5.2

BEAST is a cross-platform program for Bayesian inference using MCMC of
molecular sequences. It is entirely orientated towards rooted, time-
measured phylogenies inferred using strict or relaxed molecular clock
models. It can be used as a method of reconstructing phylogenies but is
also a framework for testing evolutionary hypotheses without
conditioning on a single tree topology.

Homepage: http://beast2.org/

BIO

boost

1.54.0

Boost provides free peer-reviewed portable C++ source libraries, emphasizing libraries that work well with the C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. The Boost license encourages both commercial and non-commercial use.

Homepage: https://www.boost.org/

T

cmake

3.15.0

A cross-platform, open-source build system. CMake is a family of tools
designed to build, test and package software.

Homepage: https://www.cmake.org

T

cuda

10.0.130

CUDA is a parallel computing platform and programming model invented by NVIDIA. It enables dramatic increases in computing performance by
harnessing the power of the graphics processing unit (GPU).

Homepage: https://developer.nvidia.com/cuda-zone

T

cudnn

7.5.1-10.0

NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural
networks

Homepage: https://developer.nvidia.com/cudnn

T

curl

7.63.0

cURL is an open source command line tool and library for transferring
data with URL syntax

Homepage: http://curl.haxx.se

T

ffmpeg

4.1.1

FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video.

Homepage: https://ffmpeg.org/

IO

fftw

3.3.8

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications.

Homepage: http://fftw.org/

MATH

gcc

5.4.0 / 9.1.0

The GNU Compiler Collection includes front ends for C, C++, Objective-C,
Fortran, Ada, and Go, as well as libraries for these languages.

Homepage: https://gcc.gnu.org

T

git

2.21.0

Git is a free and open source distributed version control system
designed to handle everything from small to very large projects with
speed and efficiency.

Homepage: http://git-scm.com

T

gnuplot

5.2.5 / python 3.7.3

Gnuplot is a portable command-line driven graphing utility for Linux,
OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is
copyrighted but freely distributed (i.e., you don't have to pay for it).
It was originally created to allow scientists and students to visualize
mathematical functions and data interactively, but has grown to support
many non-interactive uses such as web scripting. It is also used as a
plotting engine by third-party applications like Octave. Gnuplot has
been supported and under active development since 1986

Homepage: http://www.gnuplot.info

VIS

gromacs

5.1.4

GROMACS (GROningen MAchine for Chemical Simulations) is a molecular
dynamics package primarily designed for simulations of proteins, lipids
and nucleic acids. It was originally developed in the Biophysical
Chemistry department of University of Groningen, and is now maintained
by contributors in universities and research centers across the world.
GROMACS is one of the fastest and most popular software packages
available and can run on CPUs as well as GPUs. It is free, open source
released under the GNU General Public License. Starting from version
4.6, GROMACS is released under the GNU Lesser General Public License.

Homepage: http://www.gromacs.org

CHEM

gsl

2.5

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.

Homepage: https://www.gnu.org/software/gsl/

MATH

hdf5

1.10.5

HDF5 is a data model, library, and file format for storing and managing
data. It supports an unlimited variety of datatypes, and is designed for
flexible and efficient I/O and for high volume and complex data.

Homepage: https://support.hdfgroup.org/HDF5/

IO

intel-parallel-studio

professional.2019.4

Intel Parallel Studio.

Homepage: https://software.intel.com/en-us/intel-parallel-studio-xe

T

intel-mkl

2019.3.199

Intel Math Kernel Library.

Homepage: https://software.intel.com/en-us/intel-mkl

T / MATH

jdk

12.0.2.10

The Java Development Kit (JDK) released by Oracle Corporation in the
form of a binary product aimed at Java developers. Includes a complete
JRE plus tools for developing, debugging, and monitoring Java
applications.

Homepage: http://www.oracle.com/technetwork/java/javase/downloads/index.html

T

lammps

20190605

LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. This package uses patch releases, not stable release. See https://github.com/spack/spack/pull/5342 for a detailed discussion.

Homepage: https://lammps.sandia.gov/

CHEM

libx11

1.6.7

libX11 - Core X11 protocol client library.

Homepage: https://www.x.org/

T

libszip

2.1.1

Szip is an implementation of the extended-Rice lossless compression algorithm. It provides lossless compression of scientific data, and is provided with HDF software products.

Homepage: http://www.hdfgroup.org/doc_resource/SZIP/

T

libxt

1.1.5

libXt - X Toolkit Intrinsics library.

Homepage: http://cgit.freedesktop.org/xorg/lib/libXt

T

libxmu

1.1.2

This library contains miscellaneous utilities and is not part of the Xlib standard. It contains routines which only use public interfaces so that it may be layered on top of any proprietary implementation of Xlib or Xt.

T

matlab

2014a/2018b/2019b

MATLAB (MATrix LABoratory) is a multi-paradigm numerical computing
environment and fourth-generation programming language. A proprietary
programming language developed by MathWorks, MATLAB allows matrix
manipulations, plotting of functions and data, implementation of
algorithms, creation of user interfaces, and interfacing with programs
written in other languages, including C, C++, C#, Java, Fortran and
Python.

Homepage: https://www.mathworks.com/products/matlab.html

T

mercurial

4.4.1 / python 2.7.16

Mercurial is a free, distributed source control management tool.

Homepage: https://www.mercurial-scm.org

T

mesa-glu

9.0.0

This package provides the Mesa OpenGL Utility library.

Homepage: https://www.mesa3d.org

VIS

mesa

18.3.6

Mesa is an open-source implementation of the OpenGL specification - a
system for rendering interactive 3D graphics.

Homepage: http://www.mesa3d.org

VIS

metis

5.1.0

METIS is a set of serial programs for partitioning graphs, partitioning
finite element meshes, and producing fill reducing orderings for sparse
matrices. The algorithms implemented in METIS are based on the
multilevel recursive-bisection, multilevel k-way, and multi-constraint
partitioning schemes.

Homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview

MATH

netcdf

4.6.3

NetCDF is a set of software libraries and self-describing, machine-
independent data formats that support the creation, access, and sharing
of array-oriented scientific data.

Homepage: http://www.unidata.ucar.edu/software/netcdf

IO

netcdf-cxx

4.2

Deprecated C++ compatibility bindings for NetCDF. These do NOT read or
write NetCDF-4 files, and are no longer maintained by Unidata.
Developers should migrate to current NetCDF C++ bindings, in Spack
package netcdf-cxx4.

Homepage: http://www.unidata.ucar.edu/software/netcdf

IO

netcdf-fortran

4.4.5

Fortran interface for NetCDF4

Homepage: http://www.unidata.ucar.edu/software/netcdf

IO

netlib-lapack

3.8.0

LAPACK version 3.X is a comprehensive FORTRAN library that does linear
algebra operations including matrix inversions, least squared solutions
to linear sets of equations, eigenvector analysis, singular value
decomposition, etc. It is a very comprehensive and reputable package
that has found extensive use in the scientific community.

Homepage: http://www.netlib.org/lapack/

MATH

netlib-xblas

1.0.248

XBLAS is a reference implementation for extra precision BLAS. XBLAS is a
reference implementation for the dense and banded BLAS routines, along
with extended and mixed precision version. Extended precision is only
used internally; input and output arguments remain the same as in the
existing BLAS. Extra precisions is implemented as double-double (i.e.,
128-bit total, 106-bit significand). Mixed precision permits some
input/output arguments of different types (mixing real and complex) or
precisions (mixing single and double). This implementation is proof of
concept, and no attempt was made to optimize performance; performance
should be as good as straightforward but careful code written by hand.

Homepage: http://www.netlib.org/xblas

MATH

numactl

2.0.12

NUMA support for Linux

Homepage: http://oss.sgi.com/projects/libnuma/

T

miniconda2

4.6.14

The minimalist bootstrap toolset for conda and Python2.

Homepage: https://conda.io/miniconda.html

T

miniconda3

4.6.14

The minimalist bootstrap toolset for conda and Python3.

Homepage: https://conda.io/miniconda.html

T

openblas

0.3.6

OpenBLAS: An optimized BLAS library

Homepage: http://www.openblas.net

MATH

openfoam-org

3.0.1/5.0

OpenFOAM is a GPL-opensource C++ CFD-toolbox. The openfoam.org release is managed by the OpenFOAM Foundation Ltd as a licensee of the OPENFOAM trademark. This offering is not approved or endorsed by OpenCFD Ltd, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM trademark.

Homepage: https://www.openfoam.org

PHYS

openmpi

3.1.4

An open source Message Passing Interface implementation. The Open MPI
Project is an open source Message Passing Interface implementation that
is developed and maintained by a consortium of academic, research, and
industry partners. Open MPI is therefore able to combine the expertise,
technologies, and resources from all across the High Performance
Computing community in order to build the best MPI library available.
Open MPI offers advantages for system and software vendors, application
developers and computer science researchers.

Homepage: http://www.open-mpi.org

M

parallel

20190222

GNU parallel is a shell tool for executing jobs in parallel using one or
more computers. A job can be a single command or a small script that has
to be run for each of the lines in the input.

Homepage: http://www.gnu.org/software/parallel/

T

parallel-netcdf

1.11.1

PnetCDF (Parallel netCDF) is a high-performance parallel I/O library for
accessing files in format compatibility with Unidata's NetCDF,
specifically the formats of CDF-1, 2, and 5.

Homepage: https://parallel-netcdf.github.io/

IO

parmetis

4.0.3

ParMETIS is an MPI-based parallel library that implements a variety of
algorithms for partitioning unstructured graphs, meshes, and for
computing fill-reducing orderings of sparse matrices.

Homepage: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview

MATH

perl-uri

1.72

Uniform Resource Identifiers (absolute and relative)

Homepage: http://search.cpan.org/~ether/URI-1.72/lib/URI.pm

T

perl

5.26.2

Perl 5 is a highly capable, feature-rich programming language with over
27 years of development.

Homepage: http://www.perl.org

T

petsc

3.11.3

PETSc is a suite of data structures and routines for the scalable
(parallel) solution of scientific applications modeled by partial
differential equations.

Homepage: http://www.mcs.anl.gov/petsc/index.html

T

picard

2.19.0

Picard is a set of command line tools for manipulating high-throughput
sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Homepage: http://broadinstitute.github.io/picard/

BIO

plink

1.07

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

Homepage: http://zzz.bwh.harvard.edu/plink/

BIO

py-argparse

1.4.0 / python 3.7.3

Python command-line parsing library.

Homepage: https://github.com/ThomasWaldmann/argparse/

T

py-cftime

1.0.3.4 / python 2.7.16 / 3.6.8 / 3.7.3

Python library for decoding time units and variable values in a netCDF file conforming to the Climate and Forecasting (CF) netCDF conventions

Homepage: https://pypi.org/project/cftime/

T

py-jupyter-client

4.4.0 / python 3.7.3

Jupyter protocol client APIs. Project Jupyter is a non-profit, open-source project, born out of the IPython Project in 2014 as it evolved to support interactive data science and scientific computing across all programming languages.

Homepage: https://jupyter.org/

T

py-jupyter-console

5.2.0 / python 3.7.3

Jupyter Terminal Console. Project Jupyter is a non-profit, open-source project, born out of the IPython Project in 2014 as it evolved to support interactive data science and scientific computing across all programming languages.

Homepage: https://jupyter.org/

T

py-jupyter-core

4.4.0 / python 3.7.3

Core Python Jupyter functionality. Project Jupyter is a non-profit, open-source project, born out of the IPython Project in 2014 as it evolved to support interactive data science and scientific computing across all programming languages.

Homepage: https://jupyter.org/

T

py-keras

2.2.4 / python 3.7.3

Deep Learning library for Python. Convnets, recurrent neural networks,
and more. Runs on Theano or TensorFlow.

Homepage: http://keras.io

AI

py-keras-applications

1.0.7 / python 3.7.3

Sample Deep Learning application in Keras. Keras depends on this package
to run properly.

Homepage: http://keras.io

AI

py-keras-preprocessing

1.0.9 / python 3.7.3

Utilities for working with image data, text data, and sequence data.

Homepage: http://keras.io

T

py-mpi4py

3.0.1 / python 3.7.3

This package provides Python bindings for the Message Passing Interface
(MPI) standard. It is implemented on top of the MPI-1/MPI-2
specification and exposes an API which grounds on the standard MPI-2 C++
bindings.

Homepage: https://pypi.python.org/pypi/mpi4py

T

py-netcdf4

1.4.2 / python 2.7.16/ 3.6.8/ 3.7.3

Python interface to the netCDF Library.

Homepage: https://pypi.org/project/netCDF4/

T

py-numpy

1.16.4 / python 2.7.16 / 3.6.8 / 3.7.3

NumPy is the fundamental package for scientific computing with Python.
It contains among other things: a powerful N-dimensional array object,
sophisticated (broadcasting) functions, tools for integrating C/C++ and
Fortran code, and useful linear algebra, Fourier transform, and random
number capabilities

Homepage: http://www.numpy.org/

MATH

py-pandas

0.24.2 / python 2.7.16 / 3.7.3

pandas is a Python package providing fast, flexible, and expressive data
structures designed to make working with relational or labeled data both
easy and intuitive. It aims to be the fundamental high-level building
block for doing practical, real world data analysis in Python.
Additionally, it has the broader goal of becoming the most powerful and
flexible open source data analysis / manipulation tool available in any
language.

Homepage: http://pandas.pydata.org/

T

py-pip

19.0.3 / python 3.6.8 / 3.7.3

The PyPA recommended tool for installing Python packages.

Homepage: https://pypi.python.org/pypi/pip

T

py-python-dateutil

2.8.0 / python 2.7.16 / 3.7.3

Extensions to the standard Python datetime module.

Homepage: https://pypi.org/project/python-dateutil/

T

py-pytz

2018.4 / python 2.7.16 / 3.7.3

World timezone definitions, modern and historical.

Homepage: https://pypi.org/project/pytz/

T

py-scikit-learn

0.21.2 / python 3.7.3

A set of python modules for machine learning and data mining.

Homepage: https://pypi.python.org/pypi/scikit-learn

AI

py-scipy

1.2.1 / python 2.7.16 / 3.7.3

SciPy (pronounced "Sigh Pie") is a Scientific Library for Python. It
provides many user-friendly and efficient numerical routines such as
routines for numerical integration and optimization.

Homepage: http://www.scipy.org/

MATH

py-setuptools

41.0.1 / python 2.7.16 / 3.6.8 / 3.7.3

A Python utility that aids in the process of downloading, building,
upgrading, installing, and uninstalling Python packages.

Homepage: https://github.com/pypa/setuptools

T

py-six

1.12.0 / python 2.7.16 / 3.7.3

Python 2 and 3 compatibility utilities.

Homepage: https://pypi.org/project/six/

T

py-theano

1.0.4 / python 3.7.3

Optimizing compiler for evaluating mathematical expressions on CPUs and
GPUs.

Homepage: http://deeplearning.net/software/theano/

T

py-virtualenv-clone

0.2.6 / python 2.7.16 / 3.6.8 / 3.7.3

A script for cloning a non-relocatable virtualenv.

Homepage: https://github.com/edwardgeorge/virtualenv-clone

T

py-virtualenv

16.4.1 / python 2.7.16 / 3.6.8 / 3.7.3

virtualenv is a tool to create isolated Python environments.

Homepage: https://virtualenv.pypa.io/

T

python

2.7.16 / 3.6.8 / 3.7.3

The Python programming language.

Homepage: https://www.python.org/

T

r-data-table

1.11.8 / python 3.7.3

Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins,
fast add/modify/delete of columns by group using no copies at all, list
columns and a fast file reader (fread). Offers a natural and flexible
syntax, for faster development.

Homepage: https://github.com/Rdatatable/data.table/wiki

T

r-dplyr

0.7.7 / python 3.7.3

A fast, consistent tool for working with data frame like objects, both
in memory and out of memory.

Homepage: https://cran.r-project.org/package=dplyr

T

r-e1071

1.6.7 / python 3.7.3

Functions for latent class analysis, short time Fourier transform, fuzzy
clustering, support vector machines, shortest path computation, bagged
clustering, naive Bayes classifier, ...

Homepage: https://cran.r-project.org/package=e1071

T

r-ggplot2

2.2.1 / python 3.7.3

An implementation of the grammar of graphics in R. It combines the
advantages of both base and lattice graphics: conditioning and shared
axes are handled automatically, and you can still build up a plot step
by step from multiple data sources. It also implements a sophisticated
multidimensional conditioning system and a consistent interface to map
data to aesthetic attributes. See http://ggplot2.org for more
information, documentation and examples.

Homepage: http://ggplot2.org/

T

r-nnet

7.3.12 / python 3.7.3

Software for feed-forward neural networks with a single hidden layer,
and for multinomial log-linear models.

Homepage: http://www.stats.ox.ac.uk/pub/MASS4/

T

r-plyr

1.8.4 / python 3.7.3

A set of tools that solves a common set of problems: you need to break a
big problem down into manageable pieces, operate on each piece and then
put all the pieces back together. For example, you might want to fit a
model to each spatial location or time point in your study, summarise
data by panels or collapse high-dimensional arrays to simpler summary
statistics. The development of 'plyr' has been generously supported by
'Becton Dickinson'.

Homepage: http://had.co.nz/plyr

T

r-randomforest

4.6.12 / python 3.7.3

Classification and regression based on a forest of trees using random
inputs.

Homepage: https://www.stat.berkeley.edu/~breiman/RandomForests/

T

r-rbokeh

0.5.0 / python 3.7.3

R interface for creating plots in Bokeh. Bokeh by Continuum Analytics.

Homepage: https://hafen.github.io/rbokeh

T

r-reshape

0.8.7 / python 3.7.3

Flexibly restructure and aggregate data using just two functions: melt
and cast.

Homepage: https://cran.r-project.org/package=reshape

T

r-reshape2

1.4.2 / python 3.7.3

Flexibly restructure and aggregate data using just two functions: melt
and dcast (or acast).

Homepage: https://github.com/hadley/reshape

T

r-rpart-plot

2.1.0 / python 3.7.3

Plot 'rpart' models. Extends plot.rpart() and text.rpart() in the
'rpart' package.

Homepage: https://cran.r-project.org/package=rpart.plot

T

r-rpart

4.1-11 / python 3.7.3

Recursive partitioning for classification, regression and survival
trees.

Homepage: https://cran.r-project.org/package=rpart

T

r-shiny

1.0.5 / python 3.7.3

Makes it incredibly easy to build interactive web applications with R.
Automatic "reactive" binding between inputs and outputs and extensive
pre-built widgets make it possible to build beautiful, responsive, and
powerful applications with minimal effort.

Homepage: http://shiny.rstudio.com/

T

r-shinydashboard

0.7.0 / python 3.7.3

Create Dashboards with 'Shiny'

Homepage: https://cran.r-project.org/package=shinydashboard

T

r-tensora

0.36 / python 3.7.3

The package provides convenience functions for advance linear algebra
with tensors and computation with datasets of tensors on a higher level
abstraction.

Homepage: https://cran.r-project.org/web/packages/tensorA/index.html

T

r

3.6.0/3.6.2 / python 3.7.3

R is 'GNU S', a freely available language and environment for
statistical computing and graphics which provides a wide variety of
statistical and graphical techniques: linear and nonlinear modelling,
statistical tests, time series analysis, classification, clustering,
etc. Please consult the R project homepage for further information.

Homepage: https://www.r-project.org

T

singularity

3.2.1

Singularity is a container technology focused on building portable
encapsulated environments to support "Mobility of Compute" For older
versions of Singularity (pre 3.0) you should use singularity-legacy,
which has a different install base (Autotools). Needs post-install
chmod/chown steps to enable full functionality. See package definition
for details.

Homepage: https://www.sylabs.io/singularity/

T

spark

2.3.0

Apache Spark is a fast and general engine for large-scale data
processing.

Homepage: http://spark.apache.org

T

stacks

2.3b

Stacks is a software pipeline for building loci from short-read
sequences, such as those generated on the Illumina platform.

Homepage: http://catchenlab.life.illinois.edu/stacks/

BIO

supernova

2.1.1

Supernova is a software package for de novo assembly from Chromium
Linked-Reads that are made from a single whole-genome library from an
individual DNA source. A key feature of Supernova is that it creates
diploid assemblies, thus separately representing maternal and paternal
chromosomes over very long distances. Almost all other methods instead
merge homologous chromosomes into single incorrect 'consensus'
sequences. Supernova is the only practical method for creating diploid
assemblies of large genomes.

Homepage: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome

BIO

superlu-dist

6.1.1

A general purpose library for the direct solution of large, sparse,
nonsymmetric systems of linear equations on high performance machines.

Homepage: http://crd-legacy.lbl.gov/~xiaoye/SuperLU/

MATH

xtensor

0.20.7

Multi-dimensional arrays with broadcasting and lazy computing

Homepage: http://quantstack.net/xtensor

T

xtensor-python

0.23.1 / python 3.7.3

Python bindings for the xtensor C++ multi-dimensional array library

Homepage: https://xtensor-python.readthedocs.io

T